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Abstract: Mass spectrometric identification of gel-separated proteins is a cornerstone of many proteomic efforts. Often the protein compositions of two neighboring lanes (typically representing the experiment and control) are compared assuming that proteins are separated only in a vertical dimension and do not spread horizontally. However, we noticed that horizontal protein spreading commonly occurs on one-dimensional polyacrylamide gels and might lead to a misleading judgment regarding the presence or absence of particular proteins even in the distantly spaced lanes. Therefore, we suggest that experimental and control samples should always be loaded on separate gels. [Copyright &y& Elsevier]

Lamp illuminants evidence the exploitation of natural resources, animal and plant domestication, commerce, religious practices and nutrition of ancient populations. However, the physicochemical analysis of their major constituent—burned, degraded and aged mixture of triacylglycerols is imprecise and may lead to ambiguous interpretations. We applied proteomics to analyze fuel deposits from eight lamps dated by 6th to 8th centuries AD that were excavated at the Astana necropolis (Xinjiang, China) and determined their origin by identifying organism-specific proteins. Proteomics evidence corroborated and detailed the assignments of source organism relying upon comparative profiling of intact triacylglycerols by shotgun lipidomics. We found that ruminant (mostly, sheep) fat, cattle ghee and sesame oil were common combustibles in Astana and concluded that sesame as an oilseed appeared in China under Tang Dynasty concomitantly with the expansion of Buddhism. [ABSTRACT FROM AUTHOR]

Abstract: We report on the geLC–MS/MS proteomics analysis of cereals and cereal food excavated in Subeixi cemetery (500–300BC) in Xinjiang, China. Proteomics provided direct evidence that at the Subexi sourdough bread was made from barley and broomcorn millet by leavening with a renewable starter comprising baker's yeast and lactic acid bacteria. The baking recipe and flour composition indicated that barley and millet bread belonged to the staple food already in the first millennium BC and suggested the role of Turpan basin as a major route for cultural communication between Western and Eastern Eurasia in antiquity. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Biological significance: We demonstrate that organic residues of thousand year old foods unearthed by archeological excavations can be analyzed by geLC–MS/MS proteomics with good representation of protein source organisms and coverage of sequences of identified proteins. In-depth look into the foods proteome identifies the food type and its individual ingredients, reveals ancient food processing technologies, projects their social and economic impact and provides evidence of intercultural communication between ancient populations. Proteomics analysis of ancient organic residues is direct, quantitative and informative and therefore has the potential to develop into a valuable, generally applicable tool in archaeometry. This article is part of a Special Issue entitled: Proteomics of non-model organisms. [Copyright &y& Elsevier]

Abstract: Cheese making has been inferred at several sites in northern Europe as early as the 6th millennium BC and was common in Egypt and Mesopotamia in 3rd millennium BC. However, the remains of ancient cheeses have never been found and recipes of ancient dairy, its production scale, social and economic impact remain poorly understood. Here we present direct proteomics evidence for the production of an earliest known cheese that was found as an organic mass associated with the mummies of Early Bronze Age cemetery of Xiaohe (1980–1450 BC) in Xinjiang, China. Kefir fermentation of ruminant milk by a symbiotic culture of Lactobacillus kefiranofaciens and other lactic acid bacteria and yeasts was the basis of robust, scalable, probiotic, lactose-free dairy and a key technological advance that introduced economic benefits of extensive herding into a semi-pastoral household of the Eastern Eurasia population already in the Early Bronze Age. [Copyright &y& Elsevier]

Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes. [ABSTRACT FROM AUTHOR]